Article
Biochemical Research Methods
Yanzheng Meng, Lin Zhang, Laizhi Zhang, Ziyu Wang, Xuanwen Wang, Chan Li, Yu Chen, Shipeng Shang, Lei Li
Summary: CysModDB is an integrated platform designed to facilitate the study of cysteine posttranslational modifications (PTMs). It brings together comprehensive CysPTM resources and analysis tools, providing researchers with online computational and analytical tools for CysPTM site prediction, gene enrichment, and sequence feature investigation.
BRIEFINGS IN BIOINFORMATICS
(2022)
Article
Biology
Jonathan G. Van Vranken, Jiaming Li, Dylan C. Mitchell, Jose Navarrete-Perea, Steven P. Gygi
Summary: Recent advances in mass spectrometry have enabled quantitative proteomics to become a powerful tool in drug discovery, with the development of solvent shift assays allowing for the establishment of target engagement and increased efficiency. Using this approach, specific targets of compounds with known mechanisms of action can be readily identified, and combining solvent proteome profiling with other methods can expand the screening capabilities for evidence of ligand binding in the proteome.
Review
Oncology
Alyssa Min Jung Kim, Macy Rose Nemeth, Seung-Oe Lim
Summary: Immunotherapy has become an important therapeutic strategy for treating various diseases, including cancer. The 4-1BB receptor has shown promise as a therapeutic target in cancer immunotherapy and has garnered significant attention and research.
FRONTIERS IN ONCOLOGY
(2022)
Review
Biochemistry & Molecular Biology
Yifei Wang, Man Tong
Summary: The posttranslational modifications (PTMs) of proteins play a critical role in protein regulation, enhancing proteome functional diversity and participating in complicated biological processes. In cancer biology, PTMs have been shown to interact with pro-tumorigenic signaling pathways, contributing to neoplastic transformation, tumor recurrence, and resistance to therapy. Cancer stemness, which maintains tumor cell self-renewal and differentiation, is essential in cancer development and therapy resistance. Understanding the PTM profile for modulating cancer stemness has shed light on the underlying mechanisms and potential therapeutic targets for gastrointestinal cancer.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Review
Oncology
Dimitra Mavridou, Konstantina Psatha, Michalis Aivaliotis
Summary: Despite ongoing efforts, the understanding of CLL molecular pathobiology, diagnosis, prognosis, and treatment remains unclear. Proteomics combined with advanced bioinformatics and drug repurposing show promise in unraveling the complex proteome heterogeneity of CLL patients. The goal is to explore individual molecular characteristics, utilize proteomics for effective therapeutic options, and integrate drug repurposing in precision medicine for better treatment outcomes.
Article
Biochemical Research Methods
Andrew G. Chambers, David C. Chain, Steve M. Sweet, Zifeng Song, Philip L. Martin, Matthew J. Ellis, Claire Rooney, Yeoun Jin Kim
Summary: This study demonstrates the potential to expand mass spectrometry-based proteomics in preclinical and clinical oncology drug development through analysis of FFPE tumor biopsies.
CLINICAL PROTEOMICS
(2023)
Article
Biochemical Research Methods
Mark P. Molloy, Cameron Hill, Matthew B. O'Rourke, Jason Chandra, Pascal Steffen, Matthew J. McKay, Dana Pascovici, Ben R. Herbert
Summary: Microsampling of patient blood using the volumetric absorptive microsampling (VAMS) device enables LC-MS proteomic analyses of dried whole blood and enhances the proteome depth compared to conventional plasma analysis. This method also allows preferential removal of proteins and is compatible with long-term stored frozen blood cell pellets. These findings are important for establishing analysis workflows in large-scale precision medicine studies.
JOURNAL OF PROTEOME RESEARCH
(2022)
Article
Microbiology
Wiep Klaas Smits, Yassene Mohammed, Arnoud H. de Ru, Valentina Cordo, Annemieke H. Friggen, Peter A. van Veelen, Paul J. Hensbergen
Summary: This study conducted a comprehensive analysis of protein phosphorylation in the Gram-positive enteropathogen Clostridioides difficile, revealing changes in protein phosphorylation levels at different growth stages and identifying important phosphosites. This provides the basis for further investigation into the impact of individual kinases on the overall phosphoproteome of C. difficile and the role of phosphorylation in C. difficile physiology and pathogenesis.
Article
Microbiology
Wiep Klaas Smits, Yassene Mohammed, Arnoud H. de Ru, Valentina Cordo', Annemieke H. Friggen, Peter A. van Veelen, Paul J. Hensbergen
Summary: This paper presents a comprehensive analysis of protein phosphorylation in the Gram-positive enteropathogen Clostridioides difficile. The study explores the extent and nature of phosphorylation events in C. difficile and identifies target proteins and phosphorylation sites. The findings provide a foundation for further research on the role of phosphorylation in C. difficile physiology and pathogenesis.
Article
Biology
Andrew J. Buckler, David Marlevi, Nikolaos T. Skenteris, Mariette Lengquist, Malin Kronqvist, Ljubica Matic, Ulf Hedin
Summary: Computational modeling could potentially be used to tailor treatment for individual patients with atherosclerosis and prevent heart attacks and strokes. In this study, a comprehensive systems biology disease model was developed based on a unique plaque proteomic dataset, and it was used to simulate individualized responses to pharmacotherapy. The simulation results showed improvements in plaque stability, indicating that proteomics-based system biology modeling could be a potential strategy for personalized management of cardiovascular disease patients.
COMPUTERS IN BIOLOGY AND MEDICINE
(2023)
Review
Biochemistry & Molecular Biology
Piengtawan Tappiban, Yining Ying, Feifei Xu, Jinsong Bao
Summary: The study focuses on the proteomics and posttranslational modifications (PTMs) of starch biosynthesis-related proteins in rice endosperm, highlighting the differential expression of these proteins in developing seeds. Most proteins involved in starch biosynthesis increase at 6-20 days after flowering and decrease under high-temperature conditions. Various PTMs, including phosphorylation, lysine acetylation, succinylation, lysine 2-hydroxyisobutyrylation, and malonylation, target starch biosynthesis proteins in rice seeds. Further research on the role of these PTMs in starch biosynthesis is ongoing.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2021)
Article
Medicine, Research & Experimental
Aneta Stachowicz, Alia Sadiq, Brian Walker, Niveda Sundararaman, Justyna Fert-Bober
Summary: This study revealed that the treatment with BB-Cl leads to increased expression of HO-1 through the Nrf2 pathway, which can prevent excessive tissue damage and provide substantial clinical benefits for the treatment of cardiac fibrosis.
BIOMEDICINE & PHARMACOTHERAPY
(2023)
Article
Engineering, Environmental
Qingwen Qin, Lutian Wang, Juan Li, Hui Jia, Jie Wang
Summary: As a factor affecting the efficiency of hollow fiber membrane filtration, air resistance is gradually being discovered. In this study, two representative strategies for air resistance control, membrane vibration and inner surface modification, were proposed. Real-time monitoring using Fiber Bragg Grating (FBG) sensing technology and ultrasonic phased array (UPA) technology showed that initial air resistance reduces filtration efficiency rapidly, but this effect diminishes as air resistance increases. Aeration combined with fiber looseness was found to inhibit air aggregation and accelerate air escape, while inner surface modification enhanced hydrophilicity, weakened air adhesion, and increased the drag force on air bubbles. Both strategies performed well in optimizing air resistance control, with flux enhancement abilities of 26.92% and 34.10%, respectively.
Review
Genetics & Heredity
Ana Martinez-Val, Ulises H. Guzman, Jesper Olsen
Summary: Proteins are essential for transmitting encoded genetic information, and proteomics aims to understand their molecular functions in a biological context. Mass spectrometry-based proteomics is the preferred technology for studying proteomes, contributing to biomarker discovery and fundamental molecular biology. This review outlines how mass spectrometry technology has evolved to study the human proteome and its posttranslational modifications in depth, and discusses the potential of single-cell resolution proteomics.
ANNUAL REVIEW OF GENOMICS AND HUMAN GENETICS
(2022)
Review
Biochemistry & Molecular Biology
Lorenzo Moretti, Davide Bizzoca, Alessandro Geronimo, Francesco Luca Moretti, Edoardo Monaco, Giuseppe Solarino, Biagio Moretti
Summary: This review discusses the significant biomarkers in the study of osteoarthritis (OA) and their role in diagnosing and predicting the progression of the disease. Biomarkers such as Periostin, CRTA1, MMPs, and molecules like ZHX3, LYVE1, and VEGF have been found to be altered in OA. The hormonal pathway, IL-1 as a biomarker, and the combination of biomarker analysis with clinical and radiological aspects are also discussed. The study of biomarkers in synovial fluid provides an additional tool for the diagnosis and staging of OA.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Review
Biochemical Research Methods
Xi Zhang
MOLECULAR & CELLULAR PROTEOMICS
(2015)
Article
Biochemical Research Methods
Erika Darrah, AeRyon Kim, Xi Zhang, Tatiana Boronina, Robert N. Cole, Andrea Fava, Jon T. Giles, Clifton O. Bingham, Michael J. Chalmers, Patrick R. Griffin, Scheherazade Sadegh-Nasseri, Antony Rosen
JOURNAL OF PROTEOME RESEARCH
(2017)
Article
Biochemical Research Methods
Xi Zhang
MOLECULAR & CELLULAR PROTEOMICS
(2016)
Article
Chemistry, Analytical
Xi Zhang, Ellen Y. T. Chien, Michael J. Chalmers, Bruce D. Pascal, Jovylyn Gatchalian, Raymond C. Stevens, Patrick R. Griffin
ANALYTICAL CHEMISTRY
(2010)
Article
Biochemistry & Molecular Biology
Xi Zhang, Carrie Hiser, Banita Tamot, Christoph Benning, Gavin E. Reid, Shelagh M. Ferguson-Miller
Article
Biochemistry & Molecular Biology
Xi Zhang, Banita Tamot, Carrie Hiser, Gavin E. Reid, Christoph Benning, Shelagh Ferguson-Miller
Article
Physics, Atomic, Molecular & Chemical
Xi Zhang, Cassie J. Fhaner, Shelagh M. Ferguson-Miller, Gavin E. Reid
INTERNATIONAL JOURNAL OF MASS SPECTROMETRY
(2012)
Article
Biochemistry & Molecular Biology
David C. Chiara, Selwyn S. Jayakar, Xiaojuan Zhou, Xi Zhang, Pavel Y. Savechenkov, Karol S. Bruzik, Keith W. Miller, Jonathan B. Cohen
JOURNAL OF BIOLOGICAL CHEMISTRY
(2013)
Article
Chemistry, Medicinal
Pavel Y. Savechenkov, Xi Zhang, David C. Chiara, Deirdre S. Stewart, Rile Ge, Xiaojuan Zhou, Douglas E. Raines, Jonathan B. Cohen, Stuart A. Forman, Keith W. Miller, Karol S. Bruzik
JOURNAL OF MEDICINAL CHEMISTRY
(2012)
Article
Biochemical Research Methods
Xi Zhang, Shelagh M. Fergulson-Miller, Gavin E. Reid
JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY
(2009)
Article
Biochemical Research Methods
Xi Zhang, Keith W. Miller
MOLECULAR & CELLULAR PROTEOMICS
(2015)
Article
Biochemistry & Molecular Biology
Zuzana Dostalova, Xiaojuan Zhou, Aiping Liu, Xi Zhang, Yinghui Zhang, Rooma Desai, Stuart A. Forman, Keith W. Miller
Article
Cell Biology
Kimmo Rantalainen, Zachary T. Berndsen, Aleksandar Antanasijevic, Torben Schiffner, Xi Zhang, Wen-Hsin Lee, Jonathan L. Torres, Lei Zhang, Adriana Irimia, Jeffrey Copps, Kenneth H. Zhou, Young D. Kwon, William H. Law, Chaim A. Schramm, Raffaello Verardi, Shelly J. Krebs, Peter D. Kwong, Nicole A. Doria-Rose, Ian A. Wilson, Michael B. Zwick, John R. Yates, William R. Schief, Andrew B. Ward
Article
Cell Biology
Li-Chun Cheng, Sabyasachi Baboo, Cory Lindsay, Liza Brusman, Salvador Martinez-Bartolome, Olga Tapia, Xi Zhang, John R. Yates, Larry Gerace